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(-) Description

Title :  CRYSTAL STRUCTURE OF L-ISOASPARTYL (D-ASPARTYL) O-METHYLTRANSFERASE WITH ADENOSINE
 
Authors :  S. C. Griffith, M. R. Sawaya, D. Boutz, N. Thapar, J. Katz, S. Clarke, T. O. Yeates
Date :  22 Jun 01  (Deposition) - 16 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossman Methyltransferase, Protein Repair Isomerization (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Griffith, M. R. Sawaya, D. R. Boutz, N. Thapar, J. E. Katz, S. Clarke, T. O. Yeates
Crystal Structure Of A Protein Repair Methyltransferase From Pyrococcus Furiosus With Its L-Isoaspartyl Peptide Substrate.
J. Mol. Biol. V. 313 1103 2001
PubMed-ID: 11700066  |  Reference-DOI: 10.1006/JMBI.2001.5095
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.77
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    SynonymPROTEIN-BETA-ASPARTATE METHYLTRANSFERASE;
PIMT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:102 , TRP A:104 , ASN A:105 , HOH A:1124 , HOH A:1126BINDING SITE FOR RESIDUE NA A 236
2AC2SOFTWAREGLN A:72 , GLY A:99 , GLY A:101 , ILE A:120 , GLU A:121 , ARG A:122 , ILE A:123 , LEU A:126 , GLY A:147 , ASP A:148 , GLY A:149 , THR A:165 , PRO A:220 , LEU A:221 , ILE A:222 , HOH A:1096 , HOH A:1128BINDING SITE FOR RESIDUE ADN A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JG2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JG2)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCMTPS01279 Protein-L-isoaspartate(D-aspartate) O-methyltransferase signature.PIMT_PYRFU137-152  1A:147-162

(-) Exons   (0, 0)

(no "Exon" information available for 1JG2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:215
 aligned with PIMT_PYRFU | Q8TZR3 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
           PIMT_PYRFU     4 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLFVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 218
               SCOP domains d1jg2a_ A: Protein-L-isoaspartyl O-methyltransferase                                                                                                                                                                    SCOP domains
               CATH domains 1jg2A00 A:14-228 Vaccinia Virus protein VP39                                                                                                                                                                            CATH domains
               Pfam domains -----PCMT-1jg2A01 A:19-226                                                                                                                                                                                           -- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....ee.....ee.hhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeee......eeeeeeeee..eeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PCMT            ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jg2 A  14 EKELYEKWMRTVEMLKAEGIIRSKEVERAFLKYPRYLSVEDKYKKYAHIDEPLPIPAGQTVSAPHMVAIMLEIANLKPGMNILEVGTGSGWNAALISEIVKTDVYTIERIPELVEFAKRNLERAGVKNVHVILGDGSKGFPPKAPYDVIIVTAGAPKIPEPLIEQLKIGGKLIIPVGSYHLWQELLEVRKTKDGIKIKNHGGVAFVPLIGEYGWK 228
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIMT_PYRFU | Q8TZR3)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004719    protein-L-isoaspartate (D-aspartate) O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-beta-aspartate = S-adenosyl-L-homocysteine + protein L-beta-aspartate methyl ester.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0030091    protein repair    The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PIMT_PYRFU | Q8TZR31jg1 1jg3 1jg4

(-) Related Entries Specified in the PDB File

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